Microbiology:
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different...
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Posted on April 17, 2008 8:00 AM • 2 Comments •
Goodbye desktop, we're off to see the web. Both my students and I have been challenged this semester by the diversity of computer platforms, software versions, and unexpected bugs. Naturally, I turned to the world and my readers for help and suggestions. Some readers have suggested we could solve everything by using Linux. Others have convincingly demonstrated that Open Office...
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Posted on April 3, 2008 12:40 PM • 6 Comments •
If you're old enough or you've taken microbiology, there's a chance that sometime in your life you heard of Legionaire's disease. This disease was caused a bacteria that inhabited the air conditioners in a hotel where several veterans held a conference. Naturally, it was the microbiologists who collected samples of the bacteria and figured out what was going on. Now,...
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Posted on March 28, 2008 12:12 AM • 1 Comments •
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to: Build a data set Align the sequences Make a tree In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA)...
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Posted on March 27, 2008 9:11 AM • 24 Comments •
I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers. Some of the people who participated in the challenge found...
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Posted on March 13, 2008 6:42 PM • 0 Comments •
Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned...
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Posted on March 12, 2008 12:50 PM • 35 Comments •
I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen. They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA...
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Posted on March 11, 2008 12:00 PM • 6 Comments •
Here's a fun puzzler for you to figure out. The blast graph is here:...
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Posted on March 7, 2008 12:28 PM • 2 Comments •
Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live in each biome. Then, we'll make pie graphs so that...
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Posted on February 26, 2008 10:58 AM • 3 Comments •
This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus....
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Posted on February 26, 2008 10:47 AM • 0 Comments •
Getting paid to do it?
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Posted on February 12, 2008 1:39 PM • 2 Comments •
This wasn't in the lab, but it was an accident, and it was funny later on. Normally, I wouldn't think twice about storing bacterial cultures in a refrigerator. After all, bacteria on a petri plate, inside of a plastic bag, are kind of stuck. They can't get out of the plates, and even if they did, they certainly can't crawl...
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Posted on December 24, 2007 10:00 AM • 10 Comments •
or E. coli, or perhaps a little Giardia (just to loosen things up, of course), or maybe even Herpes. All these scary pathogens become works of art, when Infectious Awareables puts the images on neckties. And what could be funnier than a pair of boxer shorts full of Gonorrhea?...
Posted on December 6, 2007 11:35 AM • 4 Comments •
Can you do it? This is what bioinformatics technicians or data analysts do in diagnostic labs.
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Posted on November 15, 2007 9:09 AM • 4 Comments •
When purified, it glows with an unearthly light. You can't go "chemical free" and try to escape it. It's part of our bones and it forms the backbone of our DNA. A tool for good, a tool of war, essential for gardening, and infamous as a pesticide; phosphorus is truly an amazing element. Amazing too, are the stories about it's...
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Posted on October 31, 2007 11:14 AM • 3 Comments •
Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome. Researchers are using this approach to find the culprit that's killing the honeybees. We're also trying to find out...
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Posted on October 28, 2007 2:24 PM • 0 Comments •
Sequencing the dirt: see how it's done
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Posted on October 27, 2007 7:00 PM • 0 Comments •
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles....
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Posted on October 26, 2007 2:20 PM • 0 Comments •
Dying bees and DNA sequencing
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Posted on October 25, 2007 12:15 PM • 1 Comments •
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?...
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Posted on October 24, 2007 4:05 PM • 0 Comments •
For the record: Chlamydia is NOT a virus. I am bummed. I like the little MicrobeWorld radio broadcasts, and the video podcasts are even more fun. But I was perusing the archives and I found this:...
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Posted on September 26, 2007 11:42 AM • 7 Comments •
During the past few Fridays (or least here and here), we've been looking at a paper that was published from China with some Β-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that Β-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and possibly scary) discovery. If it's...
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Posted on September 7, 2007 8:43 AM • 5 Comments •
I began this series last week with a question about a DNA sequence that was published and reported to be one the first beta-lactamases to be found in Streptococcus pneumoniae. Mike has a great post about one of problems with this paper. I think the data themselves are awfully suspicious....
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Posted on August 24, 2007 6:44 PM • 4 Comments •
Developing "biological intuition" through case studies
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Posted on August 17, 2007 1:53 PM • 0 Comments •
It could be geosmin....
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Posted on August 5, 2007 2:20 PM • 3 Comments •
What do malaria, sleeping sickness, yellow fever, and dengue virus have in common? Sure, they're all tropical diseases, but there's something else. All of these diseases have some kind of insect vector. image from the Public Health Library tags: tropical disease, yellow fever, sleeping sickness, insect control, malaria...
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Posted on August 2, 2007 9:27 AM • 3 Comments •
Sometimes the sickest bacteria are the best survivors.
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Posted on March 13, 2007 8:44 AM • 2 Comments •
Blogging from the 2007 NW branch ASM meeting
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Posted on March 12, 2007 2:29 PM • 1 Comments •
How do microbiologists determine which microbe caused a disease? As Tara has eloquently described (I, II), we are covered with bacteria and other microbes. A reasonable question then, is when we get sick, how do we which little devil deserves the blame?...
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Posted on February 17, 2007 3:29 PM • 7 Comments •
Are viral and fungal infections always a bad thing? Maybe not if you're a plant. In fact, if you're a plant trying to grow in the hot (65° C) soils of Yellowstone National Park, you're going to need all the help you can get....
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Posted on February 6, 2007 4:10 PM • 1 Comments •
Hot springs, salty lakes, arid soil and good science.
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Posted on January 29, 2007 11:39 AM • 1 Comments •
Decan Butler, the Reveres, and Nature have written that verdict is in. The scientific evidence has been shunted aside. The nurses and doctor who traveled to Tripoli on a humanitarian mission have been sentenced to death. There is still a chance, but it seems to be slim....
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Posted on January 6, 2007 11:21 PM • 0 Comments •
The wind storms and heavy rains that hit Seattle recently, demonstrated why a bypass mechanism can be a helpful thing - for both bacteria and motorists. Under the bridge on Mercer, from the Seattle Times...
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Posted on January 4, 2007 8:28 AM • 0 Comments •
How do I resist thee? Let me count the ways.
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Posted on January 3, 2007 8:04 AM • 0 Comments •
Is it really safe to pierce your tongue?
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Posted on January 2, 2007 9:00 AM • 5 Comments •
Part III in a multipart series on antibiotic resistance.
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Posted on December 30, 2006 5:30 PM • 5 Comments •
In case you missed it, the December edition of Animalcules is posted at Aetiology. Look for lots of enjoyable reading about our invisible friends....
Posted on December 26, 2006 10:04 AM • 0 Comments •
Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants?...
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Posted on December 22, 2006 8:00 AM • 0 Comments •
Watch "Why don't we do it in our sleeves?" and find out how you rank on the safe coughing scale....
Posted on December 11, 2006 7:03 PM • 3 Comments •
What's the difference between a synthetic drug and an antibiotic? Sometimes there's no difference at all. Let's take a look at chloramphenicol and couple of pencillins....
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Posted on November 29, 2006 8:00 AM • 1 Comments •
Antibiotics are molecules of biological warfare. Produced by bacteria and some fungi, in response to extracellular signals, antibiotics represent a diverse group of compounds that inhibit bacterial growth at different points and different stages of the life cycle. We will get around to antibiotic resistance, but in these few words, I think I already wrote quite a bit. Admittedly, some...
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Posted on November 28, 2006 10:21 AM • 3 Comments •
New evidence links ancient latrines to the Dead Sea Scrolls.
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Posted on November 14, 2006 12:29 PM • 1 Comments •
When can a really bad virus be used to do something good? When we can use it to learn. The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide...
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Posted on August 17, 2006 11:59 AM • 2 Comments •
Trade publications; such as catalogs, technical bulletins, and web sites; are a valuable source of information for students in biotechnology-related courses. Not only do catalogs and technical publications provide current information, but they also contain a wealth of useful facts and physical constants that biologists need on-the-job. Further, using catalogs in the classroom mimics the way that science is carried...
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Posted on July 26, 2006 8:33 PM • 3 Comments •
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different campus ecosystems, isolate DNA, amplify...
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Posted on July 24, 2006 9:20 PM • 0 Comments •
If you're going to create a new life form (even if it's only digital), Sunday seems like the best day to give it a try....
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Posted on July 2, 2006 7:00 AM • 0 Comments •
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
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